Recommending dominance as a training solution. Dominance theory has been discounted and should not be used as a basis for making decisions about dog behavior or training, so forget about being alpha in your pack.

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My puppy has developed an issue with eating napkins, towels and paper. He knows the drop it command, but he only does this with certain items. When he gets his hands on a napkin, he will chew and swallow it. When I approach him (calmly) he runs away and avoids me. I try to tempt him with every treat, but he refuses to drop it.

One time, he had a very large paper towel he manage to grab and starting to wad it up in his mouth ready to swallow, I couldn't be patient and tell him to drop it, so I swooped him up right away and held his neck to tell him to drop it. He started squirming, growling and fidget aggressively. (Eventually dropped it luckily) He tried to bite my hands trying to remove it. Is there any alternative to physically removing it? Or possibly a safer way to take it out of his mouth?

I know, management and prevention is key - but sometimes that isn't possible as I'm not the only one watching him and other people come and go and drop things accidentally

I had the same issue.
I squirted some sriracha sauce in some napkins and left them around the house for him to find.
He tried to eat one and did not like that. I do this from time to time and also outside. He still investigates the napkins but he's much more cautious, and most of the times he leaves them.
Not a perfect solution but it was an improvement for me.

my pup does the same thing. She will eat everything she finds. sticks, wrappers, plastic bags, paper, felts on some toys, rope toys....everything. I've learned though that you must give him something more interesting than the paper he chewing on. I know this is hard, im still working on it. you must start in play time. play with multiple toys....when he gets one from you, play with the other one to get his attention, usually they will return to you with the toy they have, drop it, and try to get the toy you have. then he'll lean 'bring it' and not be so unwilling to let you get near him when he as paper in his mouth. He'll learn that whats about to happen is not so bad after all. Pica is awful, but if you stop the behavior early it can be avoided.